Seed storage protein gene promoters contain conserved DNA motifs in <it>Brassicaceae</it>, <it>Fabaceae </it>and <it>Poaceae</it>
<p>Abstract</p> <p>Background</p> <p>Accurate computational identification of <it>cis</it>-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting...
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doaj-090ecfecdfe6418eadc73ec55ab134cb2020-11-24T23:39:29ZengBMCBMC Plant Biology1471-22292009-10-019112610.1186/1471-2229-9-126Seed storage protein gene promoters contain conserved DNA motifs in <it>Brassicaceae</it>, <it>Fabaceae </it>and <it>Poaceae</it>Fauteux FrançoisStrömvik Martina V<p>Abstract</p> <p>Background</p> <p>Accurate computational identification of <it>cis</it>-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of <it>cis</it>-regulatory motifs.</p> <p>Results</p> <p>We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely <it>Brassicaceae </it>(mustards), <it>Fabaceae </it>(legumes) and <it>Poaceae </it>(grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (<it>Arabidopsis thaliana </it>(L.) Heynh.), soybean (<it>Glycine max </it>(L.) Merr.) and rice (<it>Oryza sativa </it>L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in <it>Brassicaceae </it>and <it>Fabaceae </it>SSP gene promoters that are similar to experimentally characterized seed-specific <it>cis</it>-regulatory elements. <it>Fabaceae </it>SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in <it>Poaceae </it>SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins.</p> <p>Conclusion</p> <p>Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs. The majority of discovered motifs match experimentally characterized <it>cis</it>-regulatory elements. These results provide a good starting point for further experimental analysis of plant seed-specific promoters and our methodology can be used to unravel more transcriptional regulatory mechanisms in plants and other eukaryotes.</p> http://www.biomedcentral.com/1471-2229/9/126 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Fauteux François Strömvik Martina V |
spellingShingle |
Fauteux François Strömvik Martina V Seed storage protein gene promoters contain conserved DNA motifs in <it>Brassicaceae</it>, <it>Fabaceae </it>and <it>Poaceae</it> BMC Plant Biology |
author_facet |
Fauteux François Strömvik Martina V |
author_sort |
Fauteux François |
title |
Seed storage protein gene promoters contain conserved DNA motifs in <it>Brassicaceae</it>, <it>Fabaceae </it>and <it>Poaceae</it> |
title_short |
Seed storage protein gene promoters contain conserved DNA motifs in <it>Brassicaceae</it>, <it>Fabaceae </it>and <it>Poaceae</it> |
title_full |
Seed storage protein gene promoters contain conserved DNA motifs in <it>Brassicaceae</it>, <it>Fabaceae </it>and <it>Poaceae</it> |
title_fullStr |
Seed storage protein gene promoters contain conserved DNA motifs in <it>Brassicaceae</it>, <it>Fabaceae </it>and <it>Poaceae</it> |
title_full_unstemmed |
Seed storage protein gene promoters contain conserved DNA motifs in <it>Brassicaceae</it>, <it>Fabaceae </it>and <it>Poaceae</it> |
title_sort |
seed storage protein gene promoters contain conserved dna motifs in <it>brassicaceae</it>, <it>fabaceae </it>and <it>poaceae</it> |
publisher |
BMC |
series |
BMC Plant Biology |
issn |
1471-2229 |
publishDate |
2009-10-01 |
description |
<p>Abstract</p> <p>Background</p> <p>Accurate computational identification of <it>cis</it>-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of <it>cis</it>-regulatory motifs.</p> <p>Results</p> <p>We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely <it>Brassicaceae </it>(mustards), <it>Fabaceae </it>(legumes) and <it>Poaceae </it>(grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (<it>Arabidopsis thaliana </it>(L.) Heynh.), soybean (<it>Glycine max </it>(L.) Merr.) and rice (<it>Oryza sativa </it>L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in <it>Brassicaceae </it>and <it>Fabaceae </it>SSP gene promoters that are similar to experimentally characterized seed-specific <it>cis</it>-regulatory elements. <it>Fabaceae </it>SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in <it>Poaceae </it>SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins.</p> <p>Conclusion</p> <p>Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs. The majority of discovered motifs match experimentally characterized <it>cis</it>-regulatory elements. These results provide a good starting point for further experimental analysis of plant seed-specific promoters and our methodology can be used to unravel more transcriptional regulatory mechanisms in plants and other eukaryotes.</p> |
url |
http://www.biomedcentral.com/1471-2229/9/126 |
work_keys_str_mv |
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